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Exam 1 Flashcards

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1
Q

What are microbiomes and why are they more important to study than individual bacteria?

A

collections of microbes
microbes tend to work collectively

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2
Q

endosymbiosis theory

A

theory that eukaryotic cells arose when an archaea cell consumed a bacteria (the bacteria then became the mitochondria)

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3
Q

antibiotic resistant genes can…

A

break down antibiotic
prevent access by pumping antibiotic out of the cell
change the target (by making it unrecognizable to the antibiotic)

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4
Q

what is ori?

A

origin of all single-cell replication/how single (circular) cells replicate DNA

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5
Q

conjugation

A

bacteria forms bridge –> DNA is transferred to other cell

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6
Q

transformation

A

cell picks up DNA from surrounding area

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7
Q

transduction

A

bacteriophage kills cell –> picks up DNA instead of virus –> tries to infect new cell, but deposits DNA instead

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8
Q

how does bacteria protect itself from infection via bacteriophage?

A

endonuclease: cuts off harmful DNA
methylase: adds methyl group so good DNA is not recognized by endonuclease

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9
Q

Genomics

A

field of genetics that attempts to understand the content, organization, function, and evolution of the genetic information contained in whole genomes

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10
Q

Structural genomics

A

study of the organization and sequence of the genetic information contained within a genome, providing the basic DNA sequence information that is used in functional and evolutionary studies

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11
Q

Genetic maps

A

provide a rough approximation of the locations of genes relative to the locations of other known genes

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12
Q

What are genetic maps based off of?

A

recombinant frequency - how often genes cross over (this happens more frequently when genes are far apart on same chromosome or on different chromosome) so frequency > 50% = genes are far from each other

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13
Q

Physical map

A

Map of physical distances between loci, genetic markers, or other chromosome segments; measured in base pairs

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14
Q

Map based sequencing

A

Method of sequencing a genome in which short sequenced fragments are assembled into the correct sequence in contigs with the use of genetic or physical maps

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15
Q

Contig

A

set of two or more overlapping DNA fragments that form continuous stretch of DNA

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16
Q

whole genome shotgun sequencing

A

small insert clones prepared directly from genomic DNA and sequenced

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17
Q

sequencing coverage

A

average number of times nucleotide in genome is sequenced

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18
Q

single nucleotide polymorphism

A

site in the genome where individual members of a species differ in a single base pair

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19
Q

haplotype

A

A specific set of linked genetic variants or alleles on a single chromosome or on part of a chromosome.

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20
Q

tag-SNP

A

SNPs used to identify haplotypes

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21
Q

annotation

A

Linking of a gene’s sequence information to other information about the gene’s function and expression, about the protein it encodes, and about similar genes in other species

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22
Q

What are the different forms in which viral genomes are found? What are they in the viruses in this section?

A

DNA or RNA
single-stranded (positive or negative strand) or double-stranded
linear or circular
single nucleic acid or multiple strands

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23
Q

what does host range mean?

A

right receptor for virus
(some have wide range, i.e. rabies)

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24
Q

early genes

A

involved in viral replication

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25
late genes
make viral structural proteins
26
restriction/modification enzymes
bacterial defense against bacteriophage infection
27
endonuclease
restriction enzyme that cuts incoming DNA at specific sequence, usually palindrome (soldier)
28
methylase
protects bacterial DNA by adding methyl groups to sequences, blocks the binding of endonuclease (healer)
29
what are the 3 components of nucleotides?
ribose or deoxyribose (sugar) phosphate nitrogenous base
30
purine vs pyrimidine
double ring vs single ring
31
why is the major groove in DNA significant?
bigger, which makes it accessible to proteins (so they can interact with bases)
32
RNA is single-stranded but...
it can base pair internally (fold in on itself)
33
semiconservative
DNA splits into 2 strands, each strand is used as template for new complimentary strand
34
helicase
unwind two strands of DNA
35
gyrase
makes sure DNA strands don' t supercoil when unwinding
36
primase
synthesizes a short strand of RNA (makes a primer for DNA polymerase)
37
ligase
binds molecules together
38
telemorase
adds nucleotides onto telomeres
39
which cells express telomerase?
stem cells and cancer cells
40
why is telomerase necessary?
chromosomes shorten each time they replicate short telomeres are unstable --> cells see them as broken ends that need to be repaired, causing chromosomal abnormalities
41
what are the 3 basic parts of gene structure?
upstream region (promoter) transcribed region (RNA coding) terminator (varies)
42
enhancers
increase transcription rate of gene (make transcription go faster)
43
RNA splicing
introns are removed and exons are spliced together
44
why do introns need to be removed?
introns are regions of noncoding DNA, they're not really doing anything other than preventing exons from being spliced together
45
What are the 3 main parts of mRNA structure?
5' UTR protein-coding region 3' UTR
46
Where is the poly-A tail in an mRNA structure?
after 3' UTR
47
What are the 5 different R groups in amino acids?
nonpolar polar, uncharged positively charged negatively charged aromatic
48
What are CPG islands and what does this suggest?
regions of a lot of CG - means C/methylation is important and protected from mutation
49
What is one way genes can be regulated?
insulators - blocks enhancers
50
sticky v.s. blunt ends
sticky - cleaved in a way that they can be compatible with another end (needs ligase to officially bind together) blunt - cleaved down the middle/not compatible with another end
51
gel electrophoresis
used to separate DNA or RNA by size electric current ran over gel, negatively charged DNA pulled towards positive end
52
How is DNA modified?
53
Methylation
methyl groups added to DNA effects DNA function if attached to promoter, could turn off gene caused by environmental aspects (stress, drugs, etc.)
54
siRNA
double-stranded non coding RNA
55
miRNA
single stranded non coding RNA
56
What are cloning vectors and what do you need for them?
cloning vectors are plasmids (small segments of DNA) origin of replication (ori) antibiotic-resistant gene for selection multiple cloning sites (this is a restriction site where DNA can be inserted) method of screening for recombinants
57
how does blue white selection work?
x gal added to plate cells that haven't taken up plasmid with foreign DNA (NON recombinant) will have an intact lacZ gene --> produce galactosidase if galactosidase is produced, x gal will make colonies blue (these are your nonrecombinant cells) while the recombinant ones will be white (since they can't produce galactosidase)
58
forced cloning
cut plasmid and insert enzyme
59
hybridization? what does it need?
when two pieces of single-stranded DNA or RNA bind together to form double-stranded molecule target has to be denatured first (via heat)
60
FISH?
fluorescent in situ hybridization use fluorescent probes to find where target sequences are on chromosome probe DNA labeled with florescent dye --> denature DNA --> probe DNA hybridized with DNA
61
PCR?
amplifies DNA (makes more copies of) denature template into two single strands anneal primers (new) to each strand (original) new DNA extends from primers
62
What types of genomes can you modify and how?
zygote - implant and allow to grow "regular" - replace nucleus of zygote, implant, allow to grow
63
What are knockout animals?
genetically modified to lack a gene
64
What is CRE?
recombinase enzyme, recognizes loxP sequences and deletes the sequences btwn them use CRISPR to engineer your gene of interest so loxP flanks it, gene will be deleted if CRE gene expressed in this cell
65
contig
series of overlapping DNA sequences that can be used to construct a map of original DNA sequence
66
haplotype
set of SNPs/nucleotide variants along the same chromosome that are typically inherited together (bcus they're close together on the same chromosome)
67
microarrays
compare amount of mRNA in control (og/untreated group) v.s. treated group both bind to DNA target green - control red - treated yellow - equal black - neither
68
RNA sequencing
determines how much and which types of RNA are in a sample
69
plasmid
small fragment of DNA
70
antibiotic-resistant genes are found on plasmids, how is this relevant to the spread of antibiotic-resistant genes?
plasmids can transfer from cell to cell, transferring the gene in the process
71
Does DNAse indicate active or inactive gene?
sensitivity = active gene
72
what epigenetic modification of chromatin would cause DNase 1 sensitivity?
histone acetylation: acetyl groups (H3CO) added to histones this destabilizes chromatin structure, allowing transcription to take place
73
what epigenetic modification of chromatin would completely shut down the gene (DNase 1 sensitivity)
DNA methylation (adding methyl groups to DNA) this stops transcription factors from binding to DNA
74
DNA ligase
glues DNA together by binding transcription factors
75
transcription factors
proteins that turn genes "on or off" by binding to DNA
76
what does an enhancer do? how?
increases the rate of transcription forms chromatin loops so enhancer is in close proximity to target gene
77
3 things a plasmid needs if you want to use it for cloning?
ori (origin of cell replication) antibiotic-resistant gene multiple cloning sites method of checking for recombinants (also uses different restriction enzymes)
78
reverse transcriptase
converts RNA --> DNA
79
Ti plasmid
plant plasmid (routinely inserts new DNA into plant cells)
80
inducible promoter
needs chemical to turn on gene (promoter starts transcription of gene, these need a bit of help to get started)
81
3' UTR of mRNA
nucleotides that aren't translated into amino acids --> affects stability of mRNA and helps regulate translation of mRNA protein coding sequence
82
DNA methylation region
in promoter, silences genes/regulates gene expression
83
RISC
takes strand of siRNA or miRNA to recognize complimentary strand --> activates RNase + cleaves RNA (basically uses RNA to silence gene expression)
84
TAD
limits range of enhancers

Genetics (5 decks)

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